Ok, I've been thinking about this and I thought that because some puzzles are longer than others that this may have somthing to do with the point scoring, but what do you know I got a fast time of 2mins 16 secs (I was lucky with the clues) and only got a score of 2426. So still in the dark. I have a reasonably fast processor and the time count seems to be the same as on my clock, so maybe this is the answer, the slower your computer the higher your score; as fast as I type I cannot get below 2 mins.

Well, that has been the case in alot of games here (i.e. word search). I was thinking that it also may be if you make mistakes and erase you lose points. All i know is as soon as they "fixed" this game it has been a pain in my butt.
good luck !
valarie